Light micrograph of the bladder of the carnivorous bladderwort
plant, Utricularia gibba. New research shows that the U.
gibba genome contains almost no noncoding DNA, demonstrating
that vast quantities of this so-called "junk DNA” may not be
necessary for complex life. Credit: Enrique Ibarra-Laclette and
Claudia Anahí Pérez-Torres.

IRAPUATO, MEXICO/BUFFALO, N.Y. — Genes make up about 2
percent of the human genome. The rest consists of a genetic
material known as noncoding DNA, and scientists have spent years
puzzling over why this material exists in such voluminous
quantities.

Now, a new study offers an unexpected insight: The large
majority of noncoding DNA, which is abundant in many living things,
may not actually be needed for complex life, according to research
set to appear in the journal Nature.

The clues lie in the genome of the carnivorous bladderwort
plant, Utricularia gibba.

The U. gibba genome is the smallest ever to be sequenced
from a complex, multicellular plant. The researchers who sequenced
it say that 97 percent of the genome consists of genes — bits
of DNA that code for proteins — and small pieces of DNA that
control those genes.

It appears that the plant has been busy deleting noncoding
“junk” DNA from its genetic material over many
generations, the scientists say. This may explain the difference
between bladderworts and junk-heavy species like corn and tobacco
— and humans.

The international research team, led by the Laboratorio Nacional
de Genómica para la Biodiversidad (LANGEBIO) in Mexico and
the University at Buffalo, reported its findings on May 12 in
Advanced Online Publication in Nature.

The study was directed by LANGEBIO Director and Professor Luis
Herrera-Estrella and UB Professor of Biological Sciences Victor
Albert, with contributions from scientists in the United States,
Mexico, China, Singapore, Spain and Germany.

“The big story is that only 3 percent of the
bladderwort’s genetic material is so-called
‘junk’ DNA,” Albert said. “Somehow, this
plant has purged most of what makes up plant genomes. What that
says is that you can have a perfectly good multicellular plant with
lots of different cells, organs, tissue types and flowers, and you
can do it without the junk. Junk is not needed.”

Noncoding DNA is DNA that doesn’t code for any proteins.
This includes mobile elements called jumping genes that have the
ability to copy (or cut) and paste themselves into new locations of
the genome.

Scientists have spent countless hours puzzling over why
noncoding DNA exists — and in such copious amounts. A recent
series of papers from ENCODE, a highly publicized international
research project, began to offer an explanation, saying that the
majority of noncoding DNA (about 80 percent) appeared to play a
role in biochemical functions such as regulation and promotion of
DNA conversion into its relative, RNA, which for genes, feeds into
the machinery that makes proteins.

But Herrera-Estrella, Albert and their colleagues argue that
organisms may not bulk up on genetic junk for reasons of
benefit.

Instead, they say, some species may simply have an inherent,
mechanistic bias toward deleting a great deal of noncoding DNA
while others have a built-in bias in the opposite direction —
toward DNA insertion and duplication. These biases are not due to
the fact that one way of behaving is more helpful than the other,
but because there are two innate ways to behave and all organisms
adhere to them to one degree or the other. The place that organisms
occupy on this sliding scale of forces depends in part on the
extent to which Darwin’s natural selection pressure is able
to counter or enhance these intrinsic biases.

The new U. gibba genome shows that having a bunch of
noncoding DNA is not crucial for complex life. The bladderwort is
an eccentric and complicated plant. It lives in aquatic habitats
like freshwater wetlands, and has developed corresponding, highly
specialized hunting methods. To capture prey, the plant pumps water
from tiny chambers called bladders, turning each into a vacuum that
can suck in and trap unsuspecting critters.

The U. gibba genome has about 80 million DNA base pairs
— a miniscule number compared to other complex plants —
and the deletion of noncoding DNA appears to account for most of
that size discrepancy, the researchers say. U. gibba has
about 28,500 genes, comparable to relatives like grape and tomato,
which have much larger genomes of about 490 and 780 million base
pairs, respectively.

The small size of the U. gibba genome is even more
surprising given the fact that the species has undergone three
complete genome doublings since its evolutionary lineage split from
that of tomato.

That is, at three distinct times in the course of its evolution,
the bladderwort’s genome doubled in size, with offspring
receiving two full copies of the species’ entire genome.
“This surprisingly rich history of duplication, paired with
the current small size of the bladderwort genome, is further
evidence that the plant has been prolific at deleting nonessential
DNA, but at the same time maintaining a functional set of genes
similar to those of other plant species” says
Herrera-Estrella.